Variant report

Variant	rs4742769
Chromosome Location	chr9:98584685-98584686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:98584403..98586297-chr9:98637755..98640000,3	MCF-7	breast:
2	chr9:98583596..98587083-chr9:98587311..98591492,4	MCF-7	breast:
3	chr9:98582540..98585042-chr9:98586577..98588192,2	MCF-7	breast:
4	chr9:98576423..98578313-chr9:98583202..98584976,2	K562	blood:
5	chr9:98571797..98574683-chr9:98583300..98586661,3	MCF-7	breast:
6	chr9:98584113..98586604-chr9:98610986..98613982,2	MCF-7	breast:
7	chr9:98578285..98580022-chr9:98583507..98586457,2	MCF-7	breast:
8	chr9:98583856..98586047-chr9:98617880..98619976,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12003772	0.88[ASN][1000 genomes]
rs12004258	0.85[AFR][1000 genomes]
rs12551596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12551880	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12554182	0.93[ASN][1000 genomes]
rs12555687	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16910342	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs16910409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16910427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17303073	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs17303324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280143	0.84[JPT][hapmap]
rs2297009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3739755	0.95[ASN][1000 genomes]
rs3739756	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs3991704	0.85[AFR][1000 genomes]
rs4742763	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4743327	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4743351	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4743460	0.88[ASN][1000 genomes]
rs4743469	0.81[ASN][1000 genomes]
rs55651016	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55770584	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55781050	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797980	0.88[ASN][1000 genomes]
rs55870020	0.90[AFR][1000 genomes]
rs55881510	0.91[ASN][1000 genomes]
rs56063686	0.95[ASN][1000 genomes]
rs56070531	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56110216	0.91[ASN][1000 genomes]
rs56125887	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56275194	0.90[AFR][1000 genomes]
rs56372801	0.88[ASN][1000 genomes]
rs56403401	0.91[ASN][1000 genomes]
rs57096664	0.97[ASN][1000 genomes]
rs58715455	0.91[AFR][1000 genomes]
rs59046245	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59189545	0.95[ASN][1000 genomes]
rs59510923	0.89[AFR][1000 genomes]
rs60301271	0.85[AFR][1000 genomes]
rs61036807	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61093440	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478983	0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs7021641	0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs7030427	0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs7031397	0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs7046189	0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs7047126	0.89[YRI][hapmap];0.94[AFR][1000 genomes]
rs73656542	0.89[AFR][1000 genomes]
rs73656543	0.89[AFR][1000 genomes]
rs73656554	0.89[AFR][1000 genomes]
rs73656561	0.90[AFR][1000 genomes]
rs73656564	0.90[AFR][1000 genomes]
rs7860019	0.89[YRI][hapmap];0.92[AFR][1000 genomes]
rs892647	0.89[AFR][1000 genomes]
rs9721742	0.85[ASN][1000 genomes]
rs9792431	0.88[ASN][1000 genomes]
rs9792684	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98570400-98585800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:98570400-98589200	Weak transcription	Left Ventricle	heart
3	chr9:98570400-98589200	Weak transcription	Right Ventricle	heart
4	chr9:98570400-98593200	Weak transcription	Gastric	stomach
5	chr9:98570400-98593800	Weak transcription	Right Atrium	heart
6	chr9:98570600-98585000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:98573000-98585400	Weak transcription	Thymus	Thymus
9	chr9:98576000-98596000	Weak transcription	Aorta	Aorta
10	chr9:98576800-98584800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:98577600-98585600	Weak transcription	Pancreas	Pancrea
12	chr9:98581800-98593800	Weak transcription	Fetal Intestine Small	intestine
13	chr9:98582400-98584800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:98582400-98585000	Weak transcription	Fetal Stomach	stomach
15	chr9:98582400-98585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:98582600-98584800	Weak transcription	HUVEC	blood vessel
17	chr9:98582600-98584800	Weak transcription	NHDF-Ad	bronchial
18	chr9:98582600-98586000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:98583800-98584800	Enhancers	Hela-S3	cervix
20	chr9:98583800-98586600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr9:98584200-98585800	Enhancers	Ovary	ovary
22	chr9:98584400-98584800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr9:98584400-98584800	Enhancers	NHLF	lung
24	chr9:98584400-98586000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:98584400-98586000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr9:98584400-98586200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:98584400-98586200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:98584600-98585200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:98584600-98585800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:98584600-98585800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:98584600-98585800	Enhancers	A549	lung
32	chr9:98584600-98585800	Enhancers	Osteobl	bone
33	chr9:98584600-98586000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:98584600-98586000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:98584600-98586000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr9:98584600-98586000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:98584600-98586000	Flanking Active TSS	GM12878-XiMat	blood
38	chr9:98584600-98586000	Enhancers	NH-A	brain

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